TL;DR: the marginal difference is so small that it doesn’t matter. Do whatever you feel is more convenient for yourself / the cashier. If you can lump together multiple MOs in one transaction, or have some small value debit gift cards to get rid of, get the maximum value of the MO.
Given the TL;DR, why am I writing this post? For the math of course!
Say you have 2 $500 Visa gift cards that you have acquired through mysterious means, and you are at your favorite place to get money orders. The fee for a money order of value between $500.01-1000 is $1.60. The question is, should you purchase a $998.40 money order with total value of $1000, or a $1000 money order for a total cost of $1001.60.